[2023-06-13 19:14:47,344] [INFO] DFAST_QC pipeline started.
[2023-06-13 19:14:47,349] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 19:14:47,349] [INFO] DQC Reference Directory: /var/lib/cwl/stg1246b38c-4d74-4c19-9480-7650d663f15c/dqc_reference
[2023-06-13 19:14:49,103] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 19:14:49,104] [INFO] Task started: Prodigal
[2023-06-13 19:14:49,104] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8fc7b8c-0db2-47a5-a619-977a28a83033/GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 19:14:51,858] [INFO] Task succeeded: Prodigal
[2023-06-13 19:14:51,858] [INFO] Task started: HMMsearch
[2023-06-13 19:14:51,858] [INFO] Running command: hmmsearch --tblout GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1246b38c-4d74-4c19-9480-7650d663f15c/dqc_reference/reference_markers.hmm GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 19:14:52,168] [INFO] Task succeeded: HMMsearch
[2023-06-13 19:14:52,169] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf8fc7b8c-0db2-47a5-a619-977a28a83033/GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-13 19:14:52,195] [INFO] Query marker FASTA was written to GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 19:14:52,195] [INFO] Task started: Blastn
[2023-06-13 19:14:52,195] [INFO] Running command: blastn -query GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg1246b38c-4d74-4c19-9480-7650d663f15c/dqc_reference/reference_markers.fasta -out GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:14:52,766] [INFO] Task succeeded: Blastn
[2023-06-13 19:14:52,770] [INFO] Selected 19 target genomes.
[2023-06-13 19:14:52,771] [INFO] Target genome list was writen to GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 19:14:52,791] [INFO] Task started: fastANI
[2023-06-13 19:14:52,791] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8fc7b8c-0db2-47a5-a619-977a28a83033/GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 19:14:59,036] [INFO] Task succeeded: fastANI
[2023-06-13 19:14:59,036] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1246b38c-4d74-4c19-9480-7650d663f15c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 19:14:59,036] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1246b38c-4d74-4c19-9480-7650d663f15c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 19:14:59,038] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 19:14:59,038] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 19:14:59,038] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-13 19:14:59,039] [INFO] DFAST Taxonomy check result was written to GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 19:14:59,040] [INFO] ===== Taxonomy check completed =====
[2023-06-13 19:14:59,040] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 19:14:59,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1246b38c-4d74-4c19-9480-7650d663f15c/dqc_reference/checkm_data
[2023-06-13 19:14:59,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 19:14:59,064] [INFO] Task started: CheckM
[2023-06-13 19:14:59,064] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 19:15:13,372] [INFO] Task succeeded: CheckM
[2023-06-13 19:15:13,373] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 19:15:13,392] [INFO] ===== Completeness check finished =====
[2023-06-13 19:15:13,392] [INFO] ===== Start GTDB Search =====
[2023-06-13 19:15:13,393] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 19:15:13,393] [INFO] Task started: Blastn
[2023-06-13 19:15:13,393] [INFO] Running command: blastn -query GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg1246b38c-4d74-4c19-9480-7650d663f15c/dqc_reference/reference_markers_gtdb.fasta -out GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:15:14,134] [INFO] Task succeeded: Blastn
[2023-06-13 19:15:14,138] [INFO] Selected 19 target genomes.
[2023-06-13 19:15:14,138] [INFO] Target genome list was writen to GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 19:15:14,175] [INFO] Task started: fastANI
[2023-06-13 19:15:14,175] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8fc7b8c-0db2-47a5-a619-977a28a83033/GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 19:15:19,111] [INFO] Task succeeded: fastANI
[2023-06-13 19:15:19,115] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 19:15:19,115] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_000437395.1	s__CAG-288 sp000437395	98.5264	471	589	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-288;g__CAG-288	95.0	99.04	98.49	0.94	0.89	6	conclusive
GCA_000433315.1	s__CAG-345 sp000433315	77.6739	72	589	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-288;g__CAG-345	95.0	99.47	99.43	0.95	0.94	3	-
--------------------------------------------------------------------------------
[2023-06-13 19:15:19,117] [INFO] GTDB search result was written to GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 19:15:19,118] [INFO] ===== GTDB Search completed =====
[2023-06-13 19:15:19,121] [INFO] DFAST_QC result json was written to GCA_938024305.1_ERR209583_bin.64_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 19:15:19,121] [INFO] DFAST_QC completed!
[2023-06-13 19:15:19,121] [INFO] Total running time: 0h0m32s